Musings on Science

Programmable Bacteria

A good bit of the news that I get is through Facebook, when geek friends post about something cool and techy. Like this article about programmable bacteria.

I want to figure out in what ways this science article succeeds and in what ways it doesn’t, and maybe — with my limited knowledge — talk about some of the nuances and the implications of it.

The CNN Article

The article begins with a short, snappy phrase — “bacteria that can be programmed like a computer” — and then goes on to describe how the logic gates are built from genes instead of wires and metal (I assume the quotation marks around “logic gates” isn’t to express skepticism but to illustrate that the genes were just acting like logic gates). Then the article talks about digital processing, and in just the third paragraph, leaps straight into the implications of such a programmable bacteria colony.

First of all, this is incredibly cool and more than a little exciting. If I’m understanding this correctly, the genetic code of simple organisms like bacteria can be programmed to act like the digital logic gates of an electronic circuit such as can be found in computers. So, say we want someone who’s diabetic (which usually means that you’re not producing nearly enough insulin, a hormone that controls the level of sugar in your body) to start producing more insulin — I suppose cells could now be “re-programmed” to respond to certain types of input (like too much sugar?) and that would artificially create insulin. Or perhaps they could just grow vats of pre-programmed bacteria which would produce natural chemical hormones.

The thing is, this sort of application is never explained in the article. They seem to simply go from “here’s a rough idea” to “here’s what we can do fifty years later”. “The findings hold promise for fields such as agriculture and the pharmaceutical industry,” says the CNN piece. But how promise? What promise?

Perhaps that might be easier to understand if we had been told what a logic gate actually is, how the genes could be rearranged to create such a logic gate, and what sorts of example inputs and outputs the bacteria colony would be producing. How is that colony linked up by the logic gates, anyway?

CNN, unfortunately, didn’t link to the academic paper in the article. Additional information on mathematical models, figures, etc can be found here. There are pros and cons to this: on the one hand, if you’re able to read the paper, you might realize that they were hyping it up a bit and we won’t be able to cure cancer by mere thought or something, decades into the future. On the other hand, a far more prosaic and realistic reason could be that most of these articles which are about to be published aren’t actually accessible without a (quite costly) subscription. Your average layperson certainly isn’t going to shell out thirty dollars for something that they — and this is the other crucial point — most likely won’t understand.

The Journal Abstract

But the journal abstract could tell us a few things, if we knew some basic knowledge. The journal article talks about how a NOR gate was constructed to drive promoters and repressors. This might sound like Greek, but honestly it’s not that bad. Logic gates just take in some inputs and spit out a function according to whatever they’re supposed to do. An AND gate only gives an output if both its inputs are happening at the same time. For instance, you’d go to bed only if you were sleepy AND you’d finished all your work. A NOR gate puts out some kind of positive output only if neither of the inputs is present. That sounds simple enough, but the important thing is that the NOR gate (and the NAND gate, which performs the exact reverse of the AND gate) is a “universal” gate: you can build any of the other gates, including the NAND, out of this one. That’s probably why the researchers chose to build that (again, the article doesn’t confirm that) and that’s why it’s a good thing that it appears to have worked.

And the repressors and promoters are, as far as I can tell, the means by which florescence was either turned off or turned on (respectively), which was the method the scientists were using to observe the success of their experiment.

The News Release

All that sort of information would’ve been really useful in an article of this kind, but CNN is not the only one to blame. The first source of information for science articles like this is usually the news release from the department or university itself, and it should list the purpose of the investigation, the people involved and their roles, the results and their implications. It’s basically like a science news article, except that the biases are clearly towards the scientists and the universities themselves; for instance, the press release for this included details about Voight’s previous awards or recognitions. It also included the crucial fact that Voight was not the lead author. It was, in fact, Alvin Tamsir, a fact that CNN left out entirely.

Now, looking at the news release, one thing jumps out at me: it’s not any more informative than the CNN piece itself. By this time, quite a few people know, even vaguely, that 1s and 0s form the basis of computation. The average reader is also aware that genes are what produce a lot of our individual characteristics, and that they can produce diseases which are sometimes impossible to cure (e.g. cancer). But the link between them is drawn imperfectly here. Yes, “any substrate can act like a computer”, but how is that substrate doing this?

So the press release takes on some blame as well for this sort of rather shoddy reporting. But that’s not quite fair, is it? Some CNN drone had to do their job and write this up by lunchtime and really they don’t have space or time.

If that’s your stance, go back to that article. Scroll down to the comments. If that’s representative of CNN’s readership, or representative of the average American, I’m seriously concerned for this nation.

And that’s why I think that the problem of mentioning examples, instead of vague declarations about revolutionizing pharmacy and agriculture, is something that needs to be fixed as soon as possible. Voight says, “It’s not that we’re trying to replace computers with living cells. But it means we could gain programmable control of everything biology can do. You’d like to be able to control all these programs.” To a rational, scientific-minded, reasonable skeptic, he sounds hopeful (and maybe a bit too optimistic). To those commentors, he sounds like Dr. Frankenstein. He should have either explained himself to his press team, or refrained from making hugely sweeping statements of the sort.

That, or the commentors could have been educated a little better, but that seems too much to hope for at this stage.

In the midst of this gloom and doom, however, I am able to offer some consolation: a better article! Here it is, at a site I’ve never heard of, called kqed.org. Knowledge is power, folks. Enjoy! 🙂